BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617504.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 32,000,000 number of mapped reads = 30,434,415 (95.11%) number of supplementary alignments = 166,687 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,371,636 number of mapped paired reads (second in pair) = 15,062,779 number of mapped paired reads (both in pair) = 29,830,956 number of mapped paired reads (singletons) = 603,459 number of mapped bases = 2,961,397,681 bp number of sequenced bases = 2,959,620,912 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,297,039 duplication rate = 10% >>>>>>> Insert size mean insert size = 42,260.877 std insert size = 1,933,969.4015 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.6909 >>>>>>> ACTG content number of A's = 872,941,744 bp (29.5%) number of C's = 598,226,551 bp (20.21%) number of T's = 873,232,189 bp (29.5%) number of G's = 612,296,732 bp (20.69%) number of N's = 2,923,696 bp (0.1%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 32,941,720 number of insertions = 446,025 mapped reads with insertion percentage = 1.44% number of deletions = 1,036,562 mapped reads with deletion percentage = 3.33% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.9566X std coverageData = 9.6693X There is a 38.16% of reference with a coverageData >= 1X There is a 20.56% of reference with a coverageData >= 2X There is a 11.59% of reference with a coverageData >= 3X There is a 6.89% of reference with a coverageData >= 4X There is a 4.25% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191142900 0.7668703060121964 9.378683622998627 chr2 243199373 306082513 1.2585662093791665 11.471122216470883 chr3 198022430 244426372 1.2343367970991972 2.2439770017770804 chr4 191154276 152828635 0.7995041397870691 6.165843723510002 chr5 180915260 189657904 1.0483245249737363 2.0910334262972237 chr6 171115067 139262747 0.8138543813912074 5.3174406940747145 chr7 159138663 228382665 1.4351174044989934 13.0957552906489 chr8 146364022 131473472 0.8982635910346874 3.808468818349709 chr9 141213431 122776146 0.869436746423929 18.385965201138795 chr10 135534747 125207355 0.9238026245771499 18.551318948756055 chr11 135006516 166945288 1.2365720777506768 12.5079151750151 chr12 133851895 129148936 0.9648644570926694 2.021047861819089 chr13 115169878 125703622 1.0914626652639157 2.142326447645996 chr14 107349540 86146826 0.8024890092682279 2.236456863684371 chr15 102531392 66879131 0.6522795574647031 1.5480372971224863 chr16 90354753 79902720 0.8843222669204795 14.686916742131892 chr17 81195210 82631263 1.0176864250982294 13.571317370841635 chr18 78077248 53130590 0.6804874833703155 17.066972097768513 chr19 59128983 35452028 0.5995710766748685 5.775234569061605 chr20 63025520 87777974 1.3927370055812311 2.7966333467393008 chr21 48129895 42661537 0.8863833382557764 3.8694871694299056 chr22 51304566 22168298 0.4320921065778044 1.2577464531180382 chrMT 16571 2073548 125.1311327017078 91.78123746466034 chrX 155270560 139227479 0.8966766075938671 4.138902336350244 chrY 59373566 10307732 0.17360810027816082 13.692803108795198